India Malawi UK
BM1 324 129 91
BM2 291 91 40
BM3 288 85 41
WCBM 39 1 16
Taxa are displayed if they had a mean relative abundance of ≥2% in BM samples at ≥1 timepoint (BM1, BM2, or BM3) in ≥1 country. Taxonomic composition of extraction controls clearly differs from that of breastmilk samples, with reduced Streptococcus abundance and increased abundance of rare taxa (grouped as ‘Other’ in the plot above).
India Malawi UK
BM1 324 129 91
BM2 291 91 40
BM3 288 85 41
WCBM 39 1 16
0-100 100-1k 1k-10k >10k
0 0 0 56
PCoA plots of Bray-Curtis distances support the view that the majority extraction controls cluster separately from breastmilk samples.
Taxa are displayed if they occurred with greater prevalence in breastmilk extraction controls than samples (Fisher’s p<0.05, as determined using decontam package).
IND MLW UK
BM1 324 129 91
BM2 291 91 40
BM3 288 85 41
extraction controls 39 1 16
For each sample, the mean distance is calculated from (i) other breastmilk samples from the same country and (ii) all breastmilk extraction controls. If the sample clusters with other samples, the ratio of these distances will be <1. If the sample clusters with extraction controls, the ratio will be >1. Overall, 144/1436 (10%) samples had a ratio of >1 based on either weighted or unweighted Bray-Curtis distances and were therfore categorised as potentially contaminated. By contrast, 0/0 (NaN%) negative extraction controls had a ratio of >1.
IND MLW UK
FALSE 835 285 172
TRUE 107 21 16
Lines display depths of 5,000, 15,000 and 50,000 sequences. Abbreviations: BM, breastmillk; BS, baby stool; MS, maternal stool.
n d5k d15k d50k
BM 1224 1201 1149 873
BS 2025 1984 1977 1927
MS 446 443 441 429
Rarefaction depth of 1.5^{4} sequences per sample retains 97.6% of infant samples, 98.9% of maternal samples, and 93.9% of breastmilk samples. Note: rarefaction depth of 25,000 used for analyses focusing specifically on stool samples.
n_samples n_taxa total_count min mean sd
ps1 (unfiltered) 4680 81278 599439742 2 128085 177663
ps2 (length) 4680 69094 596953865 2 127554 177552
ps3 (taxonomy) 4680 66231 595091220 2 127156 177351
ps4 (≥0.1% in >1) 4673 10159 581503484 2 124439 174940
ps5 (strict decontam) 4558 7439 554538470 2 121663 171108
ps6 (no duplicates) 4035 7343 514393687 2 127483 180008
ps7 (samples with ≥15k) 3789 7169 513573008 15477 135543 182866
ps8 (rarefied to 15k) 3789 7032 56835000 15000 15000 0
nsamples ntaxa total_count min av sd
ps1 (infant stool) 1856 10568 269774889 4 145353 142163
ps1 (maternal stool) 466 21698 62211349 78 133501 107906
ps1 (breastmilk) 1334 50579 146574829 13 109876 147375
Mean retention % after taxon filtering (ps5):
* Infant stools = 99.9
* Maternal stools = 96.8
* Breastmilk = 85.2
nsamples ntaxa total_count min av sd
ps7 (infant stool) 1704 4677 250977560 16522 147287 145540
ps7 (maternal stool) 441 4423 57620735 23681 130659 105046
ps7 (breastmilk) 1149 1716 109534914 15477 95331 112958
nsamples ntaxa total_count min av sd
ps7 (all stool) 2145 6423 308598295 16522 143869 138328
nsamples ntaxa total_count min_count av_count NA
ps8 (infant stool) 1704 4372 25560000 15000 15000 0
ps8 (maternal stool) 441 4332 6615000 15000 15000 0
ps8 (breastmilk) 1149 1715 17235000 15000 15000 0
Ten most frequent taxanomic assignments displayed for each group. Remaining taxa grouped as ‘other’. Bar heights represent proportion of RSVs assigned to taxon, independent of their relative abundance.
BMctrl MCctrlBM
17 15
country sample_type n_samples
1 IND week of life 1 274
2 IND week of life 7 247
3 IND week of life 11 232
4 UK week of life 1 61
5 UK week of life 7 39
6 UK week of life 11 41
7 MLW week of life 1 95
8 MLW week of life 7 81
9 MLW week of life 11 79
country sample_type R2_w p_w R2_u p_u n_runs n_samples
1 IND week of life 1 0.015 0.032 0.022 0.001 4 274
2 IND week of life 7 0.023 0.001 0.030 0.001 4 247
3 IND week of life 11 0.026 0.001 0.036 0.001 4 232
7 MLW week of life 1 0.028 0.073 0.033 0.002 3 95
8 MLW week of life 7 0.039 0.022 0.049 0.001 3 81
9 MLW week of life 11 0.038 0.028 0.044 0.001 3 79
See outputs of analysis module 1 for further details of feature table filtering process.
IND MLW UK
breastmilk 26 24 30